1
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Hao X, He S. Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Garlic (Allium sativum L.). BMC PLANT BIOLOGY 2024; 24:421. [PMID: 38760734 PMCID: PMC11102281 DOI: 10.1186/s12870-024-05018-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 04/12/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND The heat shock transcription factor (HSF) plays a crucial role in the regulatory network by coordinating responses to heat stress as well as other stress signaling pathways. Despite extensive studies on HSF functions in various plant species, our understanding of this gene family in garlic, an important crop with nutritional and medicinal value, remains limited. In this study, we conducted a comprehensive investigation of the entire garlic genome to elucidate the characteristics of the AsHSF gene family. RESULTS In this study, we identified a total of 17 AsHSF transcription factors. Phylogenetic analysis classified these transcription factors into three subfamilies: Class A (9 members), Class B (6 members), and Class C (2 members). Each subfamily was characterized by shared gene structures and conserved motifs. The evolutionary features of the AsHSF genes were investigated through a comprehensive analysis of chromosome location, conserved protein motifs, and gene duplication events. These findings suggested that the evolution of AsHSF genes is likely driven by both tandem and segmental duplication events. Moreover, the nucleotide diversity of the AsHSF genes decreased by only 0.0002% from wild garlic to local garlic, indicating a slight genetic bottleneck experienced by this gene family during domestication. Furthermore, the analysis of cis-acting elements in the promoters of AsHSF genes indicated their crucial roles in plant growth, development, and stress responses. qRT-PCR analysis, co-expression analysis, and protein interaction prediction collectively highlighted the significance of Asa6G04911. Subsequent experimental investigations using yeast two-hybridization and yeast induction experiments confirmed its interaction with HSP70/90, reinforcing its significance in heat stress. CONCLUSIONS This study is the first to unravel and analyze the AsHSF genes in garlic, thereby opening up new avenues for understanding their functions. The insights gained from this research provide a valuable resource for future investigations, particularly in the functional analysis of AsHSF genes.
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Affiliation(s)
- Xiaomeng Hao
- Institute of Neurobiology, Jining Medical University, Jining, China
| | - Shutao He
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, Beijing, China.
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2
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Liu SJ, Cai C, Cai HY, Bai YQ, Wang DY, Zhang H, Peng JG, Xie LJ. Integrated analysis of transcriptome and small RNAome reveals regulatory network of rapid and long-term response to heat stress in Rhododendron moulmainense. PLANTA 2024; 259:104. [PMID: 38551672 PMCID: PMC10980653 DOI: 10.1007/s00425-024-04375-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/03/2024] [Indexed: 04/01/2024]
Abstract
MAIN CONCLUSION The post-transcriptional gene regulatory pathway and small RNA pathway play important roles in regulating the rapid and long-term response of Rhododendron moulmainense to high-temperature stress. The Rhododendron plays an important role in maintaining ecological balance. However, it is difficult to domesticate for use in urban ecosystems due to their strict optimum growth temperature condition, and its evolution and adaptation are little known. Here, we combined transcriptome and small RNAome to reveal the rapid response and long-term adaptability regulation strategies in Rhododendron moulmainense under high-temperature stress. The post-transcriptional gene regulatory pathway plays important roles in stress response, in which the protein folding pathway is rapidly induced at 4 h after heat stress, and alternative splicing plays an important role in regulating gene expression at 7 days after heat stress. The chloroplasts oxidative damage is the main factor inhibiting photosynthesis efficiency. Through WGCNA analysis, we identified gene association patterns and potential key regulatory genes responsible for maintaining the ROS steady-state under heat stress. Finally, we found that the sRNA synthesis pathway is induced under heat stress. Combined with small RNAome, we found that more miRNAs are significantly changed under long-term heat stress. Furthermore, MYBs might play a central role in target gene interaction network of differentially expressed miRNAs in R. moulmainense under heat stress. MYBs are closely related to ABA, consistently, ABA synthesis and signaling pathways are significantly inhibited, and the change in stomatal aperture is not obvious under heat stress. Taken together, we gained valuable insights into the transplantation and long-term conservation domestication of Rhododendron, and provide genetic resources for genetic modification and molecular breeding to improve heat resistance in Rhododendron.
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Affiliation(s)
- Si-Jia Liu
- College of Architectural Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China
| | - Chang Cai
- Guizhou Provincial Key Laboratory for Information Systems of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, 550001, China
| | - Hong-Yue Cai
- College of Architectural Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China
| | - Yu-Qing Bai
- Administrative Office of Wutong Mountain National Park, Shenzhen, 518004, China
| | - Ding-Yue Wang
- Administrative Office of Wutong Mountain National Park, Shenzhen, 518004, China
| | - Hua Zhang
- College of Architectural Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China
| | - Jin-Gen Peng
- College of Architectural Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China.
| | - Li-Juan Xie
- College of Architectural Engineering, Shenzhen Polytechnic University, Shenzhen, 518055, China.
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3
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Yang C, Luo A, Lu HP, Davis SJ, Liu JX. Diurnal regulation of alternative splicing associated with thermotolerance in rice by two glycine-rich RNA-binding proteins. Sci Bull (Beijing) 2024; 69:59-71. [PMID: 38044192 DOI: 10.1016/j.scib.2023.11.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/17/2023] [Accepted: 11/21/2023] [Indexed: 12/05/2023]
Abstract
Rice (Oryza sativa L.) production is threatened by global warming associated with extreme high temperatures, and rice heat sensitivity is differed when stress occurs between daytime and nighttime. However, the underlying molecular mechanism are largely unknown. We show here that two glycine-rich RNA binding proteins, OsGRP3 and OsGRP162, are required for thermotolerance in rice, especially at nighttime. The rhythmic expression of OsGRP3/OsGRP162 peaks at midnight, and at these coincident times, is increased by heat stress. This is largely dependent on the evening complex component OsELF3-2. We next found that the double mutant of OsGRP3/OsGRP162 is strikingly more sensitive to heat stress in terms of survival rate and seed setting rate when comparing to the wild-type plants. Interestingly, the defect in thermotolerance is more evident when heat stress occurred in nighttime than that in daytime. Upon heat stress, the double mutant of OsGRP3/OsGRP162 displays globally reduced expression of heat-stress responsive genes, and increases of mRNA alternative splicing dominated by exon-skipping. This study thus reveals the important role of OsGRP3/OsGRP162 in thermotolerance in rice, and unravels the mechanism on how OsGRP3/OsGRP162 regulate thermotolerance in a diurnal manner.
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Affiliation(s)
- Chuang Yang
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Anni Luo
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Hai-Ping Lu
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Seth Jon Davis
- Department of Biology, University of York, York YO105DD, UK
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou 310027, China.
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4
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Li S, Guo W, Wang C, Tang Y, Li L, Zhang H, Li Y, Wei Z, Chen J, Sun Z. Alternative splicing impacts the rice stripe virus response transcriptome. Virology 2023; 587:109870. [PMID: 37669612 DOI: 10.1016/j.virol.2023.109870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 09/07/2023]
Abstract
Alternative splicing (AS) is an important form of post transcriptional modification present in both animals and plants. However, little information was obtained about AS events in response to plant virus infection. In this study, we conducted a genome-wide transcriptome analysis on AS change in rice infected by a devastating virus, Rice stripe virus (RSV). KEGG analysis was performed on the differentially expressed (DE) genes and differentially alternative spliced (DAS) genes. The results showed that DE genes were significantly enriched in the pathway of interaction with plant pathogens. The DAS genes were mainly enriched in basal metabolism and RNA splicing pathways. The heat map clustering showed that DEGs clusters were mainly enriched in regulation of transcription and defense response while differential transcript usage (DTU) clusters were strongly enriched in mRNA splicing and calcium binding. Overall, our results provide a fundamental basis for gene-wide AS changes in rice after RSV infection.
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Affiliation(s)
- Shanshan Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Wenbin Guo
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Chen Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yao Tang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lulu Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Hehong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yanjun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jianping Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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5
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Ma Z, Lv J, Wu W, Fu D, Lü S, Ke Y, Yang P. Regulatory network of rice in response to heat stress and its potential application in breeding strategy. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:68. [PMID: 37608925 PMCID: PMC10440324 DOI: 10.1007/s11032-023-01415-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023]
Abstract
The rapid development of global industrialization has led to serious environmental problems, among which global warming has become one of the major concerns. The gradual rise in global temperature resulted in the loss of food production, and hence a serious threat to world food security. Rice is the main crop for approximately half of the world's population, and its geographic distribution, yield, and quality are frequently reduced due to elevated temperature stress, and breeding rice varieties with tolerance to heat stress is of immense significance. Therefore, it is critical to study the molecular mechanism of rice in response to heat stress. In the last decades, large amounts of studies have been conducted focusing on rice heat stress response. Valuable information has been obtained, which not only sheds light on the regulatory network underlying this physiological process but also provides some candidate genes for improved heat tolerance breeding in rice. In this review, we summarized the studies in this field. Hopefully, it will provide some new insights into the mechanisms of rice under high temperature stress and clues for future engineering breeding of improved heat tolerance rice.
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Affiliation(s)
- Zemin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Jun Lv
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000 China
| | - Wenhua Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Dong Fu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yinggen Ke
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
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6
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Wen J, Qin Z, Sun L, Zhang Y, Wang D, Peng H, Yao Y, Hu Z, Ni Z, Sun Q, Xin M. Alternative splicing of TaHSFA6e modulates heat shock protein-mediated translational regulation in response to heat stress in wheat. THE NEW PHYTOLOGIST 2023; 239:2235-2247. [PMID: 37403528 DOI: 10.1111/nph.19100] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/30/2023] [Indexed: 07/06/2023]
Abstract
Heat stress greatly threatens crop production. Plants have evolved multiple adaptive mechanisms, including alternative splicing, that allow them to withstand this stress. However, how alternative splicing contributes to heat stress responses in wheat (Triticum aestivum) is unclear. We reveal that the heat shock transcription factor gene TaHSFA6e is alternatively spliced in response to heat stress. TaHSFA6e generates two major functional transcripts: TaHSFA6e-II and TaHSFA6e-III. TaHSFA6e-III enhances the transcriptional activity of three downstream heat shock protein 70 (TaHSP70) genes to a greater extent than does TaHSFA6e-II. Further investigation reveals that the enhanced transcriptional activity of TaHSFA6e-III is due to a 14-amino acid peptide at its C-terminus, which arises from alternative splicing and is predicted to form an amphipathic helix. Results show that knockout of TaHSFA6e or TaHSP70s increases heat sensitivity in wheat. Moreover, TaHSP70s are localized in stress granule following exposure to heat stress and are involved in regulating stress granule disassembly and translation re-initiation upon stress relief. Polysome profiling analysis confirms that the translational efficiency of stress granule stored mRNAs is lower at the recovery stage in Tahsp70s mutants than in the wild types. Our finding provides insight into the molecular mechanisms by which alternative splicing improves the thermotolerance in wheat.
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Affiliation(s)
- Jingjing Wen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhen Qin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lv Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yumei Zhang
- Qingdao Agricultural University, Qingdao, 266109, China
| | - Dongli Wang
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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7
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Usman B, Derakhshani B, Jung KH. Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2019. [PMID: 37653936 PMCID: PMC10221523 DOI: 10.3390/plants12102019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.
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Affiliation(s)
- Babar Usman
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Behnam Derakhshani
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
| | - Ki-Hong Jung
- Graduate School of Green Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (B.U.)
- Research Center for Plant Plasticity, Kyung Hee University, Yongin 17104, Republic of Korea
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8
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Kopecká R, Kameniarová M, Černý M, Brzobohatý B, Novák J. Abiotic Stress in Crop Production. Int J Mol Sci 2023; 24:ijms24076603. [PMID: 37047573 PMCID: PMC10095105 DOI: 10.3390/ijms24076603] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
The vast majority of agricultural land undergoes abiotic stress that can significantly reduce agricultural yields. Understanding the mechanisms of plant defenses against stresses and putting this knowledge into practice is, therefore, an integral part of sustainable agriculture. In this review, we focus on current findings in plant resistance to four cardinal abiotic stressors—drought, heat, salinity, and low temperatures. Apart from the description of the newly discovered mechanisms of signaling and resistance to abiotic stress, this review also focuses on the importance of primary and secondary metabolites, including carbohydrates, amino acids, phenolics, and phytohormones. A meta-analysis of transcriptomic studies concerning the model plant Arabidopsis demonstrates the long-observed phenomenon that abiotic stressors induce different signals and effects at the level of gene expression, but genes whose regulation is similar under most stressors can still be traced. The analysis further reveals the transcriptional modulation of Golgi-targeted proteins in response to heat stress. Our analysis also highlights several genes that are similarly regulated under all stress conditions. These genes support the central role of phytohormones in the abiotic stress response, and the importance of some of these in plant resistance has not yet been studied. Finally, this review provides information about the response to abiotic stress in major European crop plants—wheat, sugar beet, maize, potatoes, barley, sunflowers, grapes, rapeseed, tomatoes, and apples.
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Affiliation(s)
- Romana Kopecká
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Michaela Kameniarová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Jan Novák
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
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9
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Li JY, Yang C, Xu J, Lu HP, Liu JX. The hot science in rice research: How rice plants cope with heat stress. PLANT, CELL & ENVIRONMENT 2023; 46:1087-1103. [PMID: 36478590 DOI: 10.1111/pce.14509] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/13/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Global climate change has great impacts on plant growth and development, reducing crop productivity worldwide. Rice (Oryza sativa L.), one of the world's most important food crops, is susceptible to high-temperature stress from seedling stage to reproductive stage. In this review, we summarize recent advances in understanding the molecular mechanisms underlying heat stress responses in rice, including heat sensing and signalling, transcriptional regulation, transcript processing, protein translation, and post-translational regulation. We also highlight the irreversible effects of high temperature on reproduction and grain quality in rice. Finally, we discuss challenges and opportunities for future research on heat stress responses in rice.
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Affiliation(s)
- Jin-Yu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chuang Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jiming Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hai-Ping Lu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
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10
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Mei W, Chen W, Wang Y, Liu Z, Dong Y, Zhang G, Deng H, Liu X, Lu X, Wang F, Chen G, Tang W, Xiao Y. Exogenous Kinetin Modulates ROS Homeostasis to Affect Heat Tolerance in Rice Seedlings. Int J Mol Sci 2023; 24:ijms24076252. [PMID: 37047228 PMCID: PMC10093947 DOI: 10.3390/ijms24076252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Heat stress caused by rapidly changing climate warming has become a serious threat to crop growth worldwide. Exogenous cytokinin (CK) kinetin (KT) has been shown to have positive effects in improving salt and drought tolerance in plants. However, the mechanism of KT in heat tolerance in rice is poorly understood. Here, we found that exogenously adequate application of KT improved the heat stress tolerance of rice seedlings, with the best effect observed when the application concentration was 10−9 M. In addition, exogenous application of 10−9 M KT promoted the expression of CK-responsive OsRR genes, reduced membrane damage and reactive oxygen species (ROS) accumulation in rice, and increased the activity of antioxidant enzymes. Meanwhile, exogenous 10−9 M KT treatment significantly enhanced the expression of antioxidant enzymes, heat activation, and defense-related genes. In conclusion, exogenous KT treatment regulates heat tolerance in rice seedlings by modulating the dynamic balance of ROS in plants under heat stress.
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11
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Ren H, Bao J, Gao Z, Sun D, Zheng S, Bai J. How rice adapts to high temperatures. FRONTIERS IN PLANT SCIENCE 2023; 14:1137923. [PMID: 37008476 PMCID: PMC10063981 DOI: 10.3389/fpls.2023.1137923] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
High-temperature stress affects crop yields worldwide. Identifying thermotolerant crop varieties and understanding the basis for this thermotolerance would have important implications for agriculture, especially in the face of climate change. Rice (Oryza sativa) varieties have evolved protective strategies to acclimate to high temperature, with different thermotolerance levels. In this review, we examine the morphological and molecular effects of heat on rice in different growth stages and plant organs, including roots, stems, leaves and flowers. We also explore the molecular and morphological differences among thermotolerant rice lines. In addition, some strategies are proposed to screen new rice varieties for thermotolerance, which will contribute to the improvement of rice for agricultural production in the future.
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Affiliation(s)
- Huimin Ren
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingpei Bao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhenxian Gao
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Wheat Research Center, Shijiazhuang, China
| | - Daye Sun
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shuzhi Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jiaoteng Bai
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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12
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Integrated ATAC-Seq and RNA-Seq Data Analysis to Reveal OsbZIP14 Function in Rice in Response to Heat Stress. Int J Mol Sci 2023; 24:ijms24065619. [PMID: 36982696 PMCID: PMC10057503 DOI: 10.3390/ijms24065619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023] Open
Abstract
Transcription factors (TFs) play critical roles in mediating the plant response to various abiotic stresses, particularly heat stress. Plants respond to elevated temperatures by modulating the expression of genes involved in diverse metabolic pathways, a regulatory process primarily governed by multiple TFs in a networked configuration. Many TFs, such as WRKY, MYB, NAC, bZIP, zinc finger protein, AP2/ERF, DREB, ERF, bHLH, and brassinosteroids, are associated with heat shock factor (Hsf) families, and are involved in heat stress tolerance. These TFs hold the potential to control multiple genes, which makes them ideal targets for enhancing the heat stress tolerance of crop plants. Despite their immense importance, only a small number of heat-stress-responsive TFs have been identified in rice. The molecular mechanisms underpinning the role of TFs in rice adaptation to heat stress still need to be researched. This study identified three TF genes, including OsbZIP14, OsMYB2, and OsHSF7, by integrating transcriptomic and epigenetic sequencing data analysis of rice in response to heat stress. Through comprehensive bioinformatics analysis, we demonstrated that OsbZIP14, one of the key heat-responsive TF genes, contained a basic-leucine zipper domain and primarily functioned as a nuclear TF with transcriptional activation capability. By knocking out the OsbZIP14 gene in the rice cultivar Zhonghua 11, we observed that the knockout mutant OsbZIP14 exhibited dwarfism with reduced tiller during the grain-filling stage. Under high-temperature treatment, it was also demonstrated that in the OsbZIP14 mutant, the expression of the OsbZIP58 gene, a key regulator of rice seed storage protein (SSP) accumulation, was upregulated. Furthermore, bimolecular fluorescence complementation (BiFC) experiments uncovered a direct interaction between OsbZIP14 and OsbZIP58. Our results suggested that OsbZIP14 acts as a key TF gene through the concerted action of OsbZIP58 and OsbZIP14 during rice filling under heat stress. These findings provide good candidate genes for genetic improvement of rice but also offer valuable scientific insights into the mechanism of heat tolerance stress in rice.
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Ma Z, Li M, Zhang H, Zhao B, Liu Z, Duan S, Meng X, Li G, Guo X. Alternative Splicing of TaHsfA2-7 Is Involved in the Improvement of Thermotolerance in Wheat. Int J Mol Sci 2023; 24:ijms24021014. [PMID: 36674529 PMCID: PMC9861123 DOI: 10.3390/ijms24021014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
High temperature has severely affected plant growth and development, resulting in reduced production of crops worldwide, especially wheat. Alternative splicing (AS), a crucial post-transcriptional regulatory mechanism, is involved in the growth and development of eukaryotes and the adaptation to environmental changes. Previous transcriptome data suggested that heat shock transcription factor (Hsf) TaHsfA2-7 may form different transcripts by AS. However, it remains unclear whether this post-transcriptional regulatory mechanism of TaHsfA2-7 is related to thermotolerance in wheat (Triticum aestivum). Here, we identified a novel splice variant, TaHsfA2-7-AS, which was induced by high temperature and played a positive role in thermotolerance regulation in wheat. Moreover, TaHsfA2-7-AS is predicted to encode a small truncated TaHsfA2-7 isoform, retaining only part of the DNA-binding domain (DBD). TaHsfA2-7-AS is constitutively expressed in various tissues of wheat. Notably, the expression level of TaHsfA2-7-AS is significantly up-regulated by heat shock (HS) during flowering and grain-filling stages in wheat. Further studies showed that TaHsfA2-7-AS was localized in the nucleus but lacked transcriptional activation activity. Ectopic expression of TaHsfA2-7-AS in yeast exhibited improved thermotolerance. Compared to non-transgenic plants, overexpression of TaHsfA2-7-AS in Arabidopsis results in enhanced tolerance to heat stress. Simultaneously, we also found that TaHsfA1 is directly involved in the transcriptional regulation of TaHsfA2-7 and TaHsfA2-7-AS. In summary, our findings demonstrate the function of TaHsfA2-7-AS splicing variant in response to heat stress and establish a link between regulatory mechanisms of AS and the improvement of thermotolerance in wheat.
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Affiliation(s)
- Zhenyu Ma
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Mingyue Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Huaning Zhang
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Baihui Zhao
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Zihui Liu
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Shuonan Duan
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Xiangzhao Meng
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- Correspondence: (X.M.); (G.L.)
| | - Guoliang Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- Correspondence: (X.M.); (G.L.)
| | - Xiulin Guo
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
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14
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Wang Y, Wang Y, Chen W, Dong Y, Zhang G, Deng H, Liu X, Lu X, Wang F, Chen G, Xiao Y, Tang W. Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar "IR64" and japonica cultivar "Koshihikari" at the seedling stage. Front Genet 2023; 14:1135577. [PMID: 37153001 PMCID: PMC10160441 DOI: 10.3389/fgene.2023.1135577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/12/2023] [Indexed: 05/09/2023] Open
Abstract
Heat stress (HS) has become a major abiotic stress in rice, considering the frequency and intensity of extreme hot weather. There is an urgent need to explore the differences in molecular mechanisms of HS tolerance in different cultivars, especially in indica and japonica. In this study, we investigated the transcriptome information of IR64 (indica, IR) and Koshihikari (japonica, Kos) in response to HS at the seedling stage. From the differentially expressed genes (DEGs) consistently expressed at six time points, 599 DEGs were identified that were co-expressed in both cultivars, as well as 945 and 1,180 DEGs that were specifically expressed in IR and Kos, respectively. The results of GO and KEGG analysis showed two different HS response pathways for IR and Kos. IR specifically expressed DEGs were mainly enriched in chloroplast-related pathways, whereas Kos specifically expressed DEGs were mainly enriched in endoplasmic reticulum and mitochondria-related pathways. Meanwhile, we highlighted the importance of NO biosynthesis genes, especially nitrate reductase genes, in the HS response of IR based on protein-protein interaction networks. In addition, we found that heat shock proteins and heat shock factors play very important roles in both cultivars. This study not only provides new insights into the differences in HS responses between different subspecies of rice, but also lays the foundation for future research on molecular mechanisms and breeding of heat-tolerant cultivars.
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Affiliation(s)
- Yingfeng Wang
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Yubo Wang
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Wenjuan Chen
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Yating Dong
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Guilian Zhang
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Huabing Deng
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Xiong Liu
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Xuedan Lu
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Feng Wang
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Guihua Chen
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Yunhua Xiao
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
- *Correspondence: Yunhua Xiao, ; Wenbang Tang,
| | - Wenbang Tang
- Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
- *Correspondence: Yunhua Xiao, ; Wenbang Tang,
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15
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Hussain SS, Abbas M, Abbas S, Wei M, El-Sappah AH, Sun Y, Li Y, Ragauskas AJ, Li Q. Alternative splicing: transcriptional regulatory network in agroforestry. FRONTIERS IN PLANT SCIENCE 2023; 14:1158965. [PMID: 37123829 PMCID: PMC10132464 DOI: 10.3389/fpls.2023.1158965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/13/2023] [Indexed: 05/03/2023]
Abstract
Alternative splicing (AS) in plants plays a key role in regulating the expression of numerous transcripts from a single gene in a regulatory pathway. Variable concentrations of growth regulatory hormones and external stimuli trigger alternative splicing to switch among different growth stages and adapt to environmental stresses. In the AS phenomenon, a spliceosome causes differential transcriptional modifications in messenger RNA (mRNAs), resulting in partial or complete retention of one or more introns as compared to fully spliced mRNA. Differentially expressed proteins translated from intron-retaining messenger RNA (mRNAir) perform vital functions in the feedback mechanism. At the post-transcriptional level, AS causes the remodeling of transcription factors (TFs) by the addition or deletion of binding domains to activate and/or repress transcription. In this study, we have summarized the specific role of AS in the regulation of gene expression through repression and activation of the transcriptional regulatory network under external stimuli and switch among developmental stages.
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Affiliation(s)
- Syed Sarfaraz Hussain
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Sammar Abbas
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Mingke Wei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
| | - Arthur J. Ragauskas
- Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Chemical and Biomolecular Engineering, The University of Tennessee-Knoxville, Knoxville, TN, United States
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
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Yang Y, Yu J, Qian Q, Shang L. Enhancement of Heat and Drought Stress Tolerance in Rice by Genetic Manipulation: A Systematic Review. RICE (NEW YORK, N.Y.) 2022; 15:67. [PMID: 36562861 PMCID: PMC9789292 DOI: 10.1186/s12284-022-00614-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 12/13/2022] [Indexed: 05/11/2023]
Abstract
As a result of global warming, plants are subjected to ever-increasing abiotic stresses including heat and drought. Drought stress frequently co-occurs with heat stress as a result of water evaporation. These stressors have adverse effects on crop production, which in turn affects human food security. Rice is a major food resource grown widely in crop-producing regions throughout the world. However, increasingly common heat and drought stresses in growth regions can have negative impacts on seedling morphogenesis, reproductive organ establishment, overall yield, and quality. This review centers on responses to heat and drought stress in rice. Current knowledge of molecular regulation mechanisms is summarized. We focus on approaches to cope with heat and drought stress, both at the genetic level and from an agricultural practice perspective. This review establishes a basis for improving rice stress tolerance, grain quality, and yield for human benefit.
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Affiliation(s)
- Yingxue Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Jianping Yu
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, 102206 China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- China National Rice Research Institute (CNRRI), Chinese Academy of Agricultural Sciences, Hangzhou, 311401 China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
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17
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Yang L, Yang L, Zhao C, Liu J, Tong C, Zhang Y, Cheng X, Jiang H, Shen J, Xie M, Liu S. Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1009998. [PMID: 36311064 PMCID: PMC9608124 DOI: 10.3389/fpls.2022.1009998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Alternative splicing (AS) is an important regulatory process that affects plant development and stress responses by greatly increasing the complexity of transcriptome and proteome. To understand how the AS landscape of B. napus changes in response to abiotic stresses, we investigated 26 RNA-seq libraries, including control and treatments with cold, dehydration, salt, and abscisic acid (ABA) at two different time points, to perform comparative alternative splicing analysis. Apparently, AS events increased under all stresses except dehydration for 1 h, and intron retention was the most common AS mode. In addition, a total of 357 differential alternative splicing (DAS) genes were identified under four abiotic stresses, among which 81 DAS genes existed in at least two stresses, and 276 DAS genes were presented under only one stress. A weighted gene co-expression network analysis (WGCNA) based on the splicing isoforms, rather than the genes, pinpointed out 23 co-expression modules associated with different abiotic stresses. Among them, a number of significant hub genes were also found to be DAS genes, which encode key isoforms involved in responses to single stress or multiple stresses, including RNA-binding proteins, transcription factors, and other important genes, such as RBP45C, LHY, MYB59, SCL30A, RS40, MAJ23.10, and DWF4. The splicing isoforms of candidate genes identified in this study could be a valuable resource for improving tolerance of B. napus against multiple abiotic stresses.
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Affiliation(s)
- Lingli Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Li Yang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Chuanji Zhao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jie Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuanyuan Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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18
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Li G, Xu D, Huang G, Bi Q, Yang M, Shen H, Liu H. Analysis of Whole-Transcriptome RNA-Seq Data Reveals the Involvement of Alternative Splicing in the Drought Response of Glycyrrhiza uralensis. Front Genet 2022; 13:885651. [PMID: 35656323 PMCID: PMC9152209 DOI: 10.3389/fgene.2022.885651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/22/2022] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing (AS) is a post-transcriptional regulatory mechanism that increases protein diversity. There is growing evidence that AS plays an important role in regulating plant stress responses. However, the mechanism by which AS coordinates with transcriptional regulation to regulate the drought response in Glycyrrhiza uralensis remains unclear. In this study, we performed a genome-wide analysis of AS events in G. uralensis at different time points under drought stress using a high-throughput RNA sequencing approach. We detected 2,479 and 2,764 AS events in the aerial parts (AP) and underground parts (UP), respectively, of drought-stressed G. uralensis. Of these, last exon AS and exon skipping were the main types of AS. Overall, 2,653 genes undergoing significant AS regulation were identified from the AP and UP of G. uralensis exposed to drought for 2, 6, 12, and 24 h. Gene Ontology analyses indicated that AS plays an important role in the regulation of nitrogen and protein metabolism in the drought response of G. uralensis. Notably, the spliceosomal pathway and basal transcription factor pathway were significantly enriched with differentially spliced genes under drought stress. Genes related to splicing regulators in the AP and UP of G. uralensis responded to drought stress and underwent AS under drought conditions. In summary, our data suggest that drought-responsive AS directly and indirectly regulates the drought response of G. uralensis. Further in-depth studies on the functions and mechanisms of AS during abiotic stresses will provide new strategies for improving plant stress resistance.
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Affiliation(s)
- Guozhi Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi, China
| | - Dengxian Xu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi, China
| | - Gang Huang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi, China
| | - Quan Bi
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi, China
| | - Mao Yang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi, China
| | - Haitao Shen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi, China
| | - Hailiang Liu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi, China.,Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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Wu N, Yao Y, Xiang D, Du H, Geng Z, Yang W, Li X, Xie T, Dong F, Xiong L. A MITE variation-associated heat-inducible isoform of a heat-shock factor confers heat tolerance through regulation of JASMONATE ZIM-DOMAIN genes in rice. THE NEW PHYTOLOGIST 2022; 234:1315-1331. [PMID: 35244216 DOI: 10.1111/nph.18068] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
High temperatures cause huge yield losses in rice. Heat-shock factors (Hsfs) are key transcription factors which regulate the expression of heat stress-responsive genes, but natural variation in and functional characterization of Hsfs have seldom been reported. A significant heat response locus was detected via a genome-wide association study (GWAS) using green leaf area as an indicative trait. A miniature inverted-repeat transposable element (MITE) in the promoter of a candidate gene, HTG3 (heat-tolerance gene on chromosome 3), was found to be significantly associated with heat-induced expression of HTG3 and heat tolerance (HT). The MITE-absent variant has been selected in heat-prone rice-growing regions. HTG3a is an alternatively spliced isoform encoding a functional Hsf, and experiments using overexpression and knockout rice lines showed that HTG3a positively regulates HT at both vegetative and reproductive stages. The HTG3-regulated genes were enriched for heat shock proteins and jasmonic acid signaling. Two heat-responsive JASMONATE ZIM-DOMAIN (JAZ) genes were confirmed to be directly upregulated by HTG3a, and one of them, OsJAZ9, positively regulates HT. We conclude that HTG3 plays an important role in HT through the regulation of JAZs and other heat-responsive genes. The MITE-absent allele may be valuable for HT breeding in rice.
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Affiliation(s)
- Nai Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Yilong Yao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Denghao Xiang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Hao Du
- Institute of Crop science, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zedong Geng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Tingting Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Faming Dong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
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Bai J, Wang Y, Liu Z, Guo H, Zhang F, Guo L, Yuan S, Duan W, Li Y, Tan Z, Zhao C, Zhang L. Global survey of alternative splicing and gene modules associated with fertility regulation in a thermosensitive genic male sterile wheat. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2157-2174. [PMID: 34849734 DOI: 10.1093/jxb/erab516] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Thermosensitive genic male sterile (TGMS) wheat lines are the core of two-line hybrid systems. Understanding the mechanism that regulates male sterility in TGMS wheat lines is helpful for promoting wheat breeding. Several studies have obtained information regarding the mechanisms associated with male sterility at the transcriptional level, but it is not clear how the post-transcriptional process of alternative splicing might contribute to controlling male sterility. In this study, we performed genome-wide analyses of alternative splicing during the meiosis stage in TGMS line BS366 using PacBio and RNA-Seq hybrid sequencing. Cytological observations indicated that cytoskeleton assembly in pollen cells, calcium deposition in pollen and tapetal cells, and vesicle transport in tapetal cells were deficient in BS366. According to our cytological findings, 49 differentially spliced genes were isolated. Moreover, 25 long non-coding RNA targets and three bHLH transcription factors were identified. Weighted gene co-expression network analysis detected four candidate differentially spliced genes that had strong co-relation with the seed setting percentage, which is the direct representation of male sterility in BS366. In this study, we obtained comprehensive data regarding the alternative splicing-mediated regulation of male sterility in TGMS wheat. The candidates identified may provide the molecular basis for an improved understanding of male sterility.
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Affiliation(s)
- Jianfang Bai
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Yukun Wang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, NARA 630-0192, Japan
| | - Zihan Liu
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Haoyu Guo
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Fengting Zhang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Liping Guo
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Shaohua Yuan
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Wenjing Duan
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yanmei Li
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Zhaoguo Tan
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Changping Zhao
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Liping Zhang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
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21
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Meena S, Samtani H, Khurana P. Elucidating the functional role of heat stress transcription factor A6b (TaHsfA6b) in linking heat stress response and the unfolded protein response in wheat. PLANT MOLECULAR BIOLOGY 2022; 108:621-634. [PMID: 35305221 DOI: 10.1007/s11103-022-01252-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/07/2022] [Indexed: 05/26/2023]
Abstract
TaHsfA6b-4D relocalizes intracellularly upon heat stress and play a significant role in linking the heat stress response to unfolded-protein response so as to maintain cellular homeostasis. Heat stress transcription factors (Hsfs) play a crucial role in protecting the plants against heat stress (HS). In case of wheat, TaHsfA6b-4D (earlier known as TaHsfA2d) has been identified as a seed preferential transcription factor and its role has been shown in various abiotic stresses such as heat, salt and drought stress. In the present study, a homeologue of TaHsfA6b gene (TaHsfA6b-4A) was identified and was found to be transcriptionally inactive but it localized to the nucleus. Interestingly, TaHsfA6b-4D localized to the endoplasmic reticulum-Golgi complex and peroxisomes under non-stress conditions, but was observed to accumulate in the nucleus upon HS. The expression of TaHsfA6b-4D was upregulated by dithiothreitol (DTT), which is a known ER stress inducer. Consistent with this, Arabidopsis transgenic plants overexpressing TaHsfA6b-4D performed better on DTT containing media, which further corroborated with the increased expression of ER stress marker genes in these transgenic plants in comparison to the wild type plants. Thus, these studies together suggest that TaHsfA6b-4D may relocalize intracellularly upon heat stress and may play a significant role in linking the unfolded-protein response with heat stress response so as to maintain protein homeostasis inside the cell under heat stress.
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Affiliation(s)
- Shaloo Meena
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Harsha Samtani
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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22
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Identifying QTLs for Grain Size in a Colossal Grain Rice ( Oryza sativa L.) Line, and Analysis of Additive Effects of QTLs. Int J Mol Sci 2022; 23:ijms23073526. [PMID: 35408887 PMCID: PMC8998697 DOI: 10.3390/ijms23073526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 02/01/2023] Open
Abstract
Grain size is an important component of quality and harvest traits in the field of rice breeding. Although numerous quantitative trait loci (QTLs) of grain size in rice have been reported, the molecular mechanisms of these QTLs remain poorly understood, and further research on QTL observation and candidate gene identification is warranted. In our research, we developed a suite of F2 intercross populations from a cross of 9311 and CG. These primary populations were used to map QTLs conferring grain size, evaluated across three environments, and then subjected to bulked-segregant analysis-seq (BSA-seq). In total, 4, 11, 12 and 14 QTLs for grain length (GL), grain width (GW), 1000-grain weight (TGW), and length/width ratio (LWR), respectively, were detected on the basis of a single-environment analysis. In particular, over 200 splicing-related sites were identified by whole-genome sequencing, including one splicing-site mutation with G>A at the beginning of intron 4 on Os03g0841800 (qGL3.3), producing a smaller open reading frame, without the third and fourth exons. A previous study revealed that the loss-of-function allele caused by this splicing site can negatively regulate rice grain length. Furthermore, qTGW2.1 and qGW2.3 were new QTLs for grain width. We used the near-isogenic lines (NILs) of these GW QTLs to study their genetic effects on individuals and pyramiding, and found that they have additive effects on GW. In summary, these discoveries provide a valuable genetic resource, which will facilitate further study of the genetic polymorphism of new rice varieties in rice breeding.
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23
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Zhao D, Qi X, Zhang Y, Zhang R, Wang C, Sun T, Zheng J, Lu Y. Genome-wide analysis of the heat shock transcription factor gene family in Sorbus pohuashanensis (Hance) Hedl identifies potential candidates for resistance to abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 175:68-80. [PMID: 35180530 DOI: 10.1016/j.plaphy.2022.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/13/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Heat shock transcription factors (Hsfs) are essential regulators of plant responses to abiotic stresses, growth, and development. However, all the Hsf family members have not been identified in Sorbus pohuashanensis. Therefore, the aim of this study was to identify the Hsf family members in S. pohuashanensis and examine their expression under abiotic stress conditions through the integration of gene structure, phylogenetic relationships, chromosome location, and expression patterns. Bioinformatics-based methods, identified 33 Hsfs in S. pohuashanensis. Phylogenetic analysis of Hsfs from S. pohuashanensis and other species revealed that they were more closely related to apples and white pears, followed by Populus trichocarpa, and most distantly related to Arabidopsis. Moreover, the Hsfs were clustered into three major groups: A, B, and C. Gene structure and conserved motif analysis revealed a high degree of conservation among members of the same class. Collinearity analysis revealed that segmental duplication played an essential role in increasing the size of the SpHsfs gene family in S. pohuashanensis. Additionally, several cis-acting elements associated with growth and development, hormone response, and stress were found in the promoter region of SpHsfs genes. Furthermore, expression analysis in various tissues of S. pohuashanensis showed that the genes were closely associated with heat, drought, salt stress, growth, and developmental processes. Overall, these results provide valuable information on the evolutionary relationships of the Hsf gene family. These genes stand as strong functional candidates for further studies on the resistance of S. pohuashanensis to abiotic stresses.
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Affiliation(s)
- Dongxue Zhao
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiangyu Qi
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Yan Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Ruili Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Cong Wang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Tianxu Sun
- Shandong Institute of Territorial and Spatial Planning, Jinan, Shandong Province, 250000, China
| | - Jian Zheng
- School of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
| | - Yizeng Lu
- Shandong Provincial Center of Forest Tree Germplasm Resources, Jinan, Shandong Province, 250102, China.
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24
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Post-translational modification: a strategic response to high temperature in plants. ABIOTECH 2022; 3:49-64. [PMID: 36304199 PMCID: PMC9590526 DOI: 10.1007/s42994-021-00067-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/22/2021] [Indexed: 11/21/2022]
Abstract
With the increasing global warming, high-temperature stress is affecting plant growth and development with greater frequency. Therefore, an increasing number of studies examining the mechanism of temperature response contribute to a more optimal understanding of plant growth under environmental pressure. Post-translational modification (PTM) provides the rapid reconnection of transcriptional programs including transcription factors and signaling proteins. It is vital that plants quickly respond to changes in the environment in order to survive under stressful situations. Herein, we discuss several types of PTMs that occur in response to warm-temperature and high-temperature stress, including ubiquitination, SUMOylation, phosphorylation, histone methylation, and acetylation. This review provides a valuable resolution to this issue to enable increased crop productivity at high temperatures.
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25
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Analyzing the regulatory role of heat shock transcription factors in plant heat stress tolerance: a brief appraisal. Mol Biol Rep 2022; 49:5771-5785. [PMID: 35182323 DOI: 10.1007/s11033-022-07190-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/24/2022] [Indexed: 01/11/2023]
Abstract
An increase in ambient temperature throughout the twenty-first century has been described as a "worldwide threat" for crop production. Due to their sessile lifestyles, plants have evolved highly sophisticated and complex heat stress response (HSR) mechanisms to respond to higher temperatures. The HSR allows plants to minimize the damages caused by heat stress (HS), thus enabling cellular protection. HSR is crucial for their lifecycle and yield, particularly for plants grown in the field. At the cellular level, HSR involves the production of heat shock proteins (HSPs) and other stress-responsive proteins to counter the negative effects of HS. The expression of most HSPs is transcriptionally regulated by heat shock transcription factors (HSFs). HSFs are a group of evolutionary conserved regulatory proteins present in all eukaryotes and regulate various stress responses and biological processes in plants. In recent years, significant progress has been made in deciphering the complex regulatory network of HSFs, and several HSFs not only from model plants but also from major crops have been functionally characterized. Therefore, this review explores the progress made in this fascinating research area and debates the further potential to breed thermotolerant crop cultivars through the modulation of HSF networks. Furthermore, we discussed the role of HSFs in plant HS tolerance in a class-specific manner and shed light on their functional diversity, which is evident from their mode of action. Additionally, some research gaps have been highlighted concerning class-specific manners.
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26
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He W, Wang L, Lin Q, Yu F. Rice seed storage proteins: Biosynthetic pathways and the effects of environmental factors. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1999-2019. [PMID: 34581486 DOI: 10.1111/jipb.13176] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/27/2021] [Indexed: 05/02/2023]
Abstract
Rice (Oryza sativa L.) is the most important food crop for at least half of the world's population. Due to improved living standards, the cultivation of high-quality rice for different purposes and markets has become a major goal. Rice quality is determined by the presence of many nutritional components, including seed storage proteins (SSPs), which are the second most abundant nutrient components of rice grains after starch. Rice SSP biosynthesis requires the participation of multiple organelles and is influenced by the external environment, making it challenging to understand the molecular details of SSP biosynthesis and improve rice protein quality. In this review, we highlight the current knowledge of rice SSP biosynthesis, including a detailed description of the key molecules involved in rice SSP biosynthetic processes and the major environmental factors affecting SSP biosynthesis. The effects of these factors on SSP accumulation and their contribution to rice quality are also discussed based on recent findings. This recent knowledge suggests not only new research directions for exploring rice SSP biosynthesis but also innovative strategies for breeding high-quality rice varieties.
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Affiliation(s)
- Wei He
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha, 410004, China
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
| | - Long Wang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
| | - Qinlu Lin
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Feng Yu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China
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27
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Ling Y, Mahfouz MM, Zhou S. Pre-mRNA alternative splicing as a modulator for heat stress response in plants. TRENDS IN PLANT SCIENCE 2021; 26:1153-1170. [PMID: 34334317 DOI: 10.1016/j.tplants.2021.07.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 05/11/2023]
Abstract
The molecular responses of plants to the important abiotic stress, heat stress (HS), have been extensively studied at the transcriptional level. Alternative splicing (AS) is a post-transcriptional regulatory process in which an intron-containing gene can generate more than one mRNA variant. The impact of HS on the pre-mRNA splicing process has been reported in various eukaryotes but seldom discussed in-depth, especially in plants. Here, we review AS regulation in response to HS in different plant species. We discuss potential molecular mechanisms controlling heat-inducible AS regulation in plants and hypothesize that AS regulation participates in heat-priming establishment and HS memory maintenance. We propose that the pre-mRNA splicing variation is an important regulator of plant HS responses (HSRs).
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Affiliation(s)
- Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China; Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, PR China.
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Shuangxi Zhou
- New Zealand Institute for Plant and Food Research Limited, Hawke's Bay 4130, New Zealand
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28
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John S, Olas JJ, Mueller-Roeber B. Regulation of alternative splicing in response to temperature variation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6150-6163. [PMID: 34028544 PMCID: PMC8483784 DOI: 10.1093/jxb/erab232] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/21/2021] [Indexed: 05/08/2023]
Abstract
Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future.
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Affiliation(s)
- Sheeba John
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam, Germany
| | - Justyna Jadwiga Olas
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Correspondence: or
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
- Correspondence: or
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29
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Global Survey of the Full-Length Cabbage Transcriptome ( Brassica oleracea Var. capitata L.) Reveals Key Alternative Splicing Events Involved in Growth and Disease Response. Int J Mol Sci 2021; 22:ijms221910443. [PMID: 34638781 PMCID: PMC8508790 DOI: 10.3390/ijms221910443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/25/2022] Open
Abstract
Cabbage (Brassica oleracea L. var. capitata L.) is an important vegetable crop cultivated around the world. Previous studies of cabbage gene transcripts were primarily based on next-generation sequencing (NGS) technology which cannot provide accurate information concerning transcript assembly and structure analysis. To overcome these issues and analyze the whole cabbage transcriptome at the isoform level, PacBio RS II Single-Molecule Real-Time (SMRT) sequencing technology was used for a global survey of the full-length transcriptomes of five cabbage tissue types (root, stem, leaf, flower, and silique). A total of 77,048 isoforms, capturing 18,183 annotated genes, were discovered from the sequencing data generated through SMRT. The patterns of both alternative splicing (AS) and alternative polyadenylation (APA) were comprehensively analyzed. In total, we detected 13,468 genes which had isoforms containing APA sites and 8978 genes which underwent AS events. Moreover, 5272 long non-coding RNAs (lncRNAs) were discovered, and most exhibited tissue-specific expression. In total, 3147 transcription factors (TFs) were detected and 10 significant gene co-expression network modules were identified. In addition, we found that Fusarium wilt, black rot and clubroot infection significantly influenced AS in resistant cabbage. In summary, this study provides abundant cabbage isoform transcriptome data, which promotes reannotation of the cabbage genome, deepens our understanding of their post-transcriptional regulation mechanisms, and can be used for future functional genomic research.
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30
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Vitoriano CB, Calixto CPG. Reading between the Lines: RNA-seq Data Mining Reveals the Alternative Message of the Rice Leaf Transcriptome in Response to Heat Stress. PLANTS 2021; 10:plants10081647. [PMID: 34451692 PMCID: PMC8400768 DOI: 10.3390/plants10081647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 11/21/2022]
Abstract
Rice (Oryza sativa L.) is a major food crop but heat stress affects its yield and grain quality. To identify mechanistic solutions to improve rice yield under rising temperatures, molecular responses of thermotolerance must be understood. Transcriptional and post-transcriptional controls are involved in a wide range of plant environmental responses. Alternative splicing (AS), in particular, is a widespread mechanism impacting the stress defence in plants but it has been completely overlooked in rice genome-wide heat stress studies. In this context, we carried out a robust data mining of publicly available RNA-seq datasets to investigate the extension of heat-induced AS in rice leaves. For this, datasets of interest were subjected to filtering and quality control, followed by accurate transcript-specific quantifications. Powerful differential gene expression (DE) and differential AS (DAS) identified 17,143 and 2162 heat response genes, respectively, many of which are novel. Detailed analysis of DAS genes coding for key regulators of gene expression suggests that AS helps shape transcriptome and proteome diversity in response to heat. The knowledge resulting from this study confirmed a widespread transcriptional and post-transcriptional response to heat stress in plants, and it provided novel candidates for rapidly advancing rice breeding in response to climate change.
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31
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Sandhu J, Irvin L, Liu K, Staswick P, Zhang C, Walia H. Endoplasmic reticulum stress pathway mediates the early heat stress response of developing rice seeds. PLANT, CELL & ENVIRONMENT 2021; 44:2604-2624. [PMID: 34036580 DOI: 10.1111/pce.14103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
A transient heat stress occurring during early seed development in rice (Oryza sativa) reduces seed size by altering endosperm development. However, the relationship between the timing of the stress and specific developmental stage on heat sensitivity is not well-understood. To address this, we imposed a series of non-overlapping heat stress treatments and found that young seeds are most sensitive during the first two days after flowering. Temporal transcriptome analysis of developing, heat stressed (35°C) seeds during this window shows that Inositol-requiring enzyme 1 (IRE1)-mediated endoplasmic reticulum (ER) stress response and jasmonic acid (JA) pathways are the early (1-3 h) drivers of heat stress response. We propose that increased JA levels under heat stress may precede ER stress response as JA application promotes the spliced form of OsbZIP50, an ER response marker gene linked to IRE1-specific pathway. This study presents temporal and mechanistic insights into the role of JA and ER stress signalling during early heat stress response of rice seeds that impact both grain size and quality. Modulating the heat sensitivity of the early sensing pathways and downstream endosperm development genes can enhance rice resilience to transient heat stress events.
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Affiliation(s)
- Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Larissa Irvin
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Kan Liu
- School of Biological Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Chi Zhang
- School of Biological Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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32
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Czékus Z, Iqbal N, Pollák B, Martics A, Ördög A, Poór P. Role of ethylene and light in chitosan-induced local and systemic defence responses of tomato plants. JOURNAL OF PLANT PHYSIOLOGY 2021; 263:153461. [PMID: 34217837 DOI: 10.1016/j.jplph.2021.153461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/02/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
Plant defence responses can be triggered by the application of elicitors for example chitosan (β-1,4-linked glucosamine; CHT). It is well-known that CHT induces rapid, local production of reactive oxygen species (ROS) and nitric oxide (NO) resulting in fast stomatal closure. Systemic defence responses are based primarily on phytohormones such as ethylene (ET) and salicylic acid (SA), moreover on the expression of hormone-mediated defence genes and proteins. At the same time, these responses can be dependent also on external factors, such as light but its role was less-investigated. Based on our result in intact tomato plants (Solanum lycopersicum L.), CHT treatment not only induced significant ET emission and stomatal closure locally but also promoted significant production of superoxide which was also detectable in the distal, systemic leaves. However, these changes in ET and superoxide accumulation were detected only in wild type (WT) plants kept in light and were inhibited under darkness as well as in ET receptor Never ripe (Nr) mutants suggesting pivotal importance of ET and light in inducing resistance both locally and systemically upon CHT. Interestingly, CHT-induced NO production was mostly independent of ET or light. At the same time, expression of Pathogenesis-related 3 (PR3) was increased locally in both genotypes in the light and in WT leaves under darkness. This was also observed in distal leaves of WT plants. The CHT-induced endoplasmic reticulum (ER) stress, as well as unfolded protein response (UPR) were examined for the first time, via analysis of the lumenal binding protein (BiP). Whereas local expression of BiP was not dependent on the availability of light or ET, systemically it was mediated by ET.
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Affiliation(s)
- Zalán Czékus
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Közép Fasor 52, Hungary; Doctoral School of Biology, University of Szeged, Szeged, Hungary.
| | - Nadeem Iqbal
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Közép Fasor 52, Hungary; Doctoral School of Environmental Sciences, University of Szeged, Szeged, Hungary.
| | - Boglárka Pollák
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Közép Fasor 52, Hungary.
| | - Atina Martics
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Közép Fasor 52, Hungary.
| | - Attila Ördög
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Közép Fasor 52, Hungary.
| | - Péter Poór
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Közép Fasor 52, Hungary.
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33
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Wang L, Liu Y, Chai M, Chen H, Aslam M, Niu X, Qin Y, Cai H. Genome-wide identification, classification, and expression analysis of the HSF gene family in pineapple ( Ananas comosus). PeerJ 2021; 9:e11329. [PMID: 33987013 PMCID: PMC8086565 DOI: 10.7717/peerj.11329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/31/2021] [Indexed: 11/28/2022] Open
Abstract
Transcription factors (TFs), such as heat shock transcription factors (HSFs), usually play critical regulatory functions in plant development, growth, and response to environmental cues. However, no HSFs have been characterized in pineapple thus far. Here, we identified 22 AcHSF genes from the pineapple genome. Gene structure, motifs, and phylogenetic analysis showed that AcHSF families were distinctly grouped into three subfamilies (12 in Group A, seven in Group B, and four in Group C). The AcHSF promoters contained various cis-elements associated with stress, hormones, and plant development processes, for instance, STRE, WRKY, and ABRE binding sites. The majority of HSFs were expressed in diverse pineapple tissues and developmental stages. The expression of AcHSF-B4b/AcHSF-B4c and AcHSF-A7b/AcHSF-A1c were enriched in the ovules and fruits, respectively. Six genes (AcHSF-A1a , AcHSF-A2, AcHSF-A9a, AcHSF-B1a, AcHSF-B2a, and AcHSF-C1a) were transcriptionally modified by cold, heat, and ABA. Our results provide an overview and lay the foundation for future functional characterization of the pineapple HSF gene family.
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Affiliation(s)
- Lulu Wang
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Yanhui Liu
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Mengnan Chai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Huihuang Chen
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Mohammad Aslam
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Xiaoping Niu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Yuan Qin
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Hanyang Cai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
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Ganie SA, Reddy ASN. Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance. BIOLOGY 2021; 10:309. [PMID: 33917813 PMCID: PMC8068108 DOI: 10.3390/biology10040309] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/20/2022]
Abstract
Improvements in yield and quality of rice are crucial for global food security. However, global rice production is substantially hindered by various biotic and abiotic stresses. Making further improvements in rice yield is a major challenge to the rice research community, which can be accomplished through developing abiotic stress-resilient rice varieties and engineering durable agrochemical-independent pathogen resistance in high-yielding elite rice varieties. This, in turn, needs increased understanding of the mechanisms by which stresses affect rice growth and development. Alternative splicing (AS), a post-transcriptional gene regulatory mechanism, allows rapid changes in the transcriptome and can generate novel regulatory mechanisms to confer plasticity to plant growth and development. Mounting evidence indicates that AS has a prominent role in regulating rice growth and development under stress conditions. Several regulatory and structural genes and splicing factors of rice undergo different types of stress-induced AS events, and the functional significance of some of them in stress tolerance has been defined. Both rice and its pathogens use this complex regulatory mechanism to devise strategies against each other. This review covers the current understanding and evidence for the involvement of AS in biotic and abiotic stress-responsive genes, and its relevance to rice growth and development. Furthermore, we discuss implications of AS for the virulence of different rice pathogens and highlight the areas of further research and potential future avenues to develop climate-smart and disease-resistant rice varieties.
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Affiliation(s)
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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35
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Alternative Splicing of Heat Shock Transcription Factor 2 Regulates the Expression of Laccase Gene Family in Response to Copper in Trametes trogii. Appl Environ Microbiol 2021; 87:AEM.00055-21. [PMID: 33579682 PMCID: PMC8091107 DOI: 10.1128/aem.00055-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
White-rot fungi, especially Trametes strains, are the primary source of industrial laccases in bioenergy and bioremediation. Trametes strains express members of the laccase gene family with different physicochemical properties and expression patterns. However, the literature on the expression pattern of the laccase gene family in T. trogii S0301 and the response mechanism to Cu2+, a key laccase inducer, in white-rot fungal strains is scarce. In the present study, we found that Cu2+ could induce the mRNAs and proteins of the two alternative splicing variants of heat shock transcription factor 2 (TtHSF2). Furthermore, the overexpression of alternative splicing variants TtHSF2α and TtHSF2β-I in the homokaryotic T. trogii S0301 strain showed opposite effects on the extracellular total laccase activity, with the maximum laccase activity of approximately 0.6 U mL-1 and 3.0 U mL-1, respectively, on the eighth day, which is 0.4 and 2.3 times that of the wild type strain. Similarly, TtHSF2α and TtHSF2β-I play opposite roles in the oxidation tolerance to H2O2 In addition, the direct binding of TtHSF2α to the promoter regions of the representative laccase isoenzymes (TtLac1 and TtLac13) and protein-protein interactions between TtHSF2α and TtHSF2β-I were detected. Our results demonstrate the crucial roles of TtHSF2 and its alternative splicing variants in response to Cu2+ We believe that these findings will deepen our understanding of alternative splicing of HSFs and their regulatory mechanism of the laccase gene family in white-rot fungi.Importance The members of laccase gene family in Trametes strains are the primary source of industrial laccase and have gained widespread attention. Increasing the yield and enzymatic properties of laccase through various methods has always been a topic worthy of attention, and there is no report on the regulation of laccase expression through HSF transcription factor engineering. Here, we found that two alternative splicing variants of TtHSF2 functioned oppositely in regulating the expression of laccase genes, and copper can induce the expression of almost all members of the laccase gene family. Most importantly, our study suggested that TtHSF2 and its alternative splicing variants are vital for copper-induced production of laccases in T. trogii S0301.
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36
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Qin-Di D, Gui-Hua J, Xiu-Neng W, Zun-Guang M, Qing-Yong P, Shiyun C, Yu-Jian M, Shuang-Xi Z, Yong-Xiang H, Yu L. High temperature-mediated disturbance of carbohydrate metabolism and gene expressional regulation in rice: a review. PLANT SIGNALING & BEHAVIOR 2021; 16:1862564. [PMID: 33470154 PMCID: PMC7889029 DOI: 10.1080/15592324.2020.1862564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Global warming has induced higher frequencies of excessively high-temperature weather episodes, which pose damage risk to rice growth and production. Past studies seldom specified how high temperature-induced carbohydrate metabolism disturbances from both source and sink affect rice fertilization and production. Here we discuss the mechanism of heat-triggered damage to rice quality and production through disturbance of carbohydrate generation and consumption under high temperatures. Furthermore, we provide strong evidence from past studies that rice varieties that maintain high photosynthesis and carbohydrate usage efficiencies under high temperatures will suffer less heat-induced damage during reproductive developmental stages. We also discuss the complexity of expressional regulation of rice genes in response to high temperatures, while highlighting the important roles of heat-inducible post-transcriptional regulations of gene expression. Lastly, we predict future directions in heat-tolerant rice breeding and also propose challenges that need to be conquered in the future.
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Affiliation(s)
- Deng Qin-Di
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Jian Gui-Hua
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Wang Xiu-Neng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Mo Zun-Guang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Peng Qing-Yong
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Chen Shiyun
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Mo Yu-Jian
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Zhou Shuang-Xi
- New Zealand Institute for Plant and Food Research Limited, Hawke’s Bay,New Zealand
| | - Huang Yong-Xiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
| | - Ling Yu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang,China
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37
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Li S, Jin S, Chen W, Yu J, Fang P, Zhou G, Li J, Jin L, Chen Y, Chen P, Pan C. Mangiferin alleviates endoplasmic reticulum stress in acute liver injury by regulating the miR-20a/miR-101a-Nrf2 axis. J Biochem 2021; 168:365-374. [PMID: 32413114 DOI: 10.1093/jb/mvaa056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 04/20/2020] [Indexed: 01/19/2023] Open
Abstract
This study aimed to investigate the mechanism of mangiferin on regulating endoplasmic reticulum (ER) stress in acute liver injury. The mouse model of acute liver injury was established by injection of LPS/D-GalN. The primary mouse hepatocytes were stimulated with LPS to induce the in vitro model. The effect of miR-20a/101a on the luciferase activity of Nrf2 3'-UTR was assessed by luciferase reporter assay. Mangiferin improved the liver function, inhibited the oxidative stress and ER stress and down-regulated the expressions of miR-20a and miR-101a in LPS/D-GalN-induced mice and LPS-induced hepatocytes. The knockdown of miR-20a and miR-101a co-operatively alleviated ER stress of LPS-induced hepatocytes. miR-20a and miR-101a both targeted Nrf2 and the over-expression of miR-20a or miR-101a decreased Nrf2 protein level, while their silences increased Nrf2 protein level. The silence of miR-20a and miR-101a promoted Nrf2 expression and inhibited the ER stress in LPS-induced hepatocytes, while the knockdown of Nrf2 reversed these effects. The over-expression of miR-20a and miR-101a eliminated the effects of mangiferin on Nrf2 protein level and ER stress in LPS-induced hepatocytes and Nrf2 over-expression altered these trends. Our findings suggest that mangiferin alleviates ER stress in acute liver injury by regulating the miR-20a/miR-101a-Nrf2 axis.
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Affiliation(s)
- Shaoxun Li
- Department of Infectious Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang, China.,Department of Infectious Disease, The Second School of Medicine, Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang China
| | - Shuanghong Jin
- Department of Infectious Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang, China.,Department of Infectious Disease, The Second School of Medicine, Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang China
| | - Weilai Chen
- Department of Neurology, Wenzhou People's Hospital, No. 57 Canghou Road, Wenzhou 325000, Zhejiang, China
| | - Jiake Yu
- Department of Infectious Disease, The Second School of Medicine, Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang China.,Department of Pediatric Hepatitis and Liver Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang, China
| | - Peipei Fang
- Department of Infectious Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang, China.,Department of Pediatric Hepatitis and Liver Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang, China
| | - Guangyao Zhou
- Department of Infectious Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang, China
| | - Jie Li
- Department of Infectious Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang, China
| | - Lingxiang Jin
- Department of Infectious Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang, China
| | - Yiping Chen
- Department of Pediatric Hepatitis and Liver Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang, China
| | - Ping Chen
- Department of Infectious Disease, Shulan Hospital, No.848 Dongxin Road, Hangzhou 310006, Zhejiang, China.,Department of Infectious Disease, The Third People's Hospital of Zhengzhou, No.136 Nanshuncheng Road, Zhengzhou 450000, Henan, China
| | - Chenwei Pan
- Department of Infectious Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang, China.,Department of Pediatric Hepatitis and Liver Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, No. 109 West College Road, Wenzhou 325027, Zhejiang, China
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38
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Prerostova S, Jarosova J, Dobrev PI, Hluskova L, Motyka V, Filepova R, Knirsch V, Gaudinova A, Kieber J, Vankova R. Heat Stress Targeting Individual Organs Reveals the Central Role of Roots and Crowns in Rice Stress Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:799249. [PMID: 35111178 PMCID: PMC8801461 DOI: 10.3389/fpls.2021.799249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/28/2021] [Indexed: 05/10/2023]
Abstract
Inter-organ communication and the heat stress (HS; 45°C, 6 h) responses of organs exposed and not directly exposed to HS were evaluated in rice (Oryza sativa) by comparing the impact of HS applied either to whole plants, or only to shoots or roots. Whole-plant HS reduced photosynthetic activity (F v /F m and QY_Lss ), but this effect was alleviated by prior acclimation (37°C, 2 h). Dynamics of HSFA2d, HSP90.2, HSP90.3, and SIG5 expression revealed high protection of crowns and roots. Additionally, HSP26.2 was strongly expressed in leaves. Whole-plant HS increased levels of jasmonic acid (JA) and cytokinin cis-zeatin in leaves, while up-regulating auxin indole-3-acetic acid and down-regulating trans-zeatin in leaves and crowns. Ascorbate peroxidase activity and expression of alternative oxidases (AOX) increased in leaves and crowns. HS targeted to leaves elevated levels of JA in roots, cis-zeatin in crowns, and ascorbate peroxidase activity in crowns and roots. HS targeted to roots increased levels of abscisic acid and auxin in leaves and crowns, cis-zeatin in leaves, and JA in crowns, while reducing trans-zeatin levels. The weaker protection of leaves reflects the growth strategy of rice. HS treatment of individual organs induced changes in phytohormone levels and antioxidant enzyme activity in non-exposed organs, in order to enhance plant stress tolerance.
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Affiliation(s)
- Sylva Prerostova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Jana Jarosova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Petre I. Dobrev
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Lucia Hluskova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Vaclav Motyka
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Roberta Filepova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Vojtech Knirsch
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Alena Gaudinova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Joseph Kieber
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Radomira Vankova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
- *Correspondence: Radomira Vankova,
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39
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Lu Y, Zhao P, Zhang A, Ma L, Xu S, Wang X. Alternative Splicing Diversified the Heat Response and Evolutionary Strategy of Conserved Heat Shock Protein 90s in Hexaploid Wheat ( Triticum aestivum L.). Front Genet 2020; 11:577897. [PMID: 33329715 PMCID: PMC7729002 DOI: 10.3389/fgene.2020.577897] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/29/2020] [Indexed: 11/13/2022] Open
Abstract
Crops are challenged by the increasing high temperature. Heat shock protein 90 (HSP90), a molecular chaperone, plays a critical role in the heat response in plants. However, the evolutionary conservation and divergence of HSP90s homeologs in polyploidy crops are largely unknown. Using the newly released hexaploid wheat reference sequence, we identified 18 TaHSP90s that are evenly distributed as homeologous genes among three wheat subgenomes, and were highly conserved in terms of sequence identity and gene structure among homeologs. Intensive time-course transcriptomes showed uniform expression and transcriptional response profiles among the three TaHSP90 homeologs. Based on the comprehensive isoforms generated by combining full-length single-molecule sequencing and Illumina short read sequencing, 126 isoforms, including 90 newly identified isoforms of TaHSP90s, were identified, and each TaHSP90 generated one to three major isoforms. Intriguingly, the numbers and the splicing modes of the major isoforms generated by three TaHSP90 homeologs were obviously different. Furthermore, the quantified expression profiles of the major isoforms generated by three TaHSP90 homeologs are also distinctly varied, exhibiting differential alternative splicing (AS) responses of homeologs. Our results showed that the AS diversified the heat response of the conserved TaHSP90s and provided a new perspective for understanding about functional conservation and divergence of homologous genes.
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Affiliation(s)
- Yunze Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Peng Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Aihua Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Lingjian Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
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40
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Xu H, Li X, Zhang H, Wang L, Zhu Z, Gao J, Li C, Zhu Y. High temperature inhibits the accumulation of storage materials by inducing alternative splicing of OsbZIP58 during filling stage in rice. PLANT, CELL & ENVIRONMENT 2020; 43:1879-1896. [PMID: 32335936 DOI: 10.1111/pce.13779] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 05/22/2023]
Abstract
High temperature (HT) has an adverse effect on rice grain filling by inhibiting the accumulation of storage materials. However, the regulatory mechanism of this inhibition remains unknown. Here, we report that Opaque2 like transcription factor OsbZIP58 is a key factor regulating storage material accumulation under HT. The OsbZIP58 gene promotes expression of many seed storage protein genes and starch synthesis genes while inhibits expression of some starch hydrolyzing α-amylase genes under HT. The loss of OsbZIP58 function leads to floury and shrunken endosperms and dramatically reduced storage materials in the seeds under HT. HT is found to affect alternative splicing of OsbZIP58, promoting the formation of the truncated OsbZIP58β protein form over the full-length OsbZIP58α protein form. The OsbZIP58β form has a lower transcriptional activity than the OsbZIP58α form, especially under HT condition. Interestingly, rice varieties with less heat sensitivity have reduced alternative splicing of OsbZIP58. Therefore, OsbZIP58 is a crucial gene in regulating storage material accumulation under HT and lower alternative splicing of OsbZIP58 may contribute to heat tolerance during grain filling.
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Affiliation(s)
- Heng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaofang Li
- Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Hua Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Liangchao Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhengge Zhu
- Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Jiping Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chunshou Li
- Institute of Crops and Utilization of Nuclear Technology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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41
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Yao S, Liang F, Gill RA, Huang J, Cheng X, Liu Y, Tong C, Liu S. A global survey of the transcriptome of allopolyploid Brassica napus based on single-molecule long-read isoform sequencing and Illumina-based RNA sequencing data. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:843-857. [PMID: 32270540 DOI: 10.1111/tpj.14754] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 03/15/2020] [Accepted: 03/18/2020] [Indexed: 05/21/2023]
Abstract
Brassica napus is a recent allopolyploid derived from the hybridization of Brassica rapa (Ar Ar ) and Brassica oleracea (Co Co ). Because of the high sequence similarity between the An and Cn subgenomes, it is difficult to provide an accurate landscape of the whole transcriptome of B. napus. To overcome this problem, we applied a single-molecule long-read isoform sequencing (Iso-Seq) technique that can produce long reads to explore the complex transcriptome of B. napus at the isoform level. From the Iso-Seq data, we obtained 147 698 non-redundant isoforms, capturing 37 403 annotated genes. A total of 18.1% (14 934/82 367) of the multi-exonic genes showed alternative splicing (AS). In addition, we identified 549 long non-coding RNAs, the majority of which displayed tissue-specific expression profiles, and detected 7742 annotated genes that possessed isoforms containing alternative polyadenylation sites. Moreover, 31 591 AS events located in open reading frames (ORFs) lead to potential protein isoforms by in-frame or frameshift changes in the ORF. Illumina RNA sequencing of five tissues that were pooled for Iso-Seq was also performed and showed that 69% of the AS events were tissue-specific. Our data provide abundant transcriptome resources for a transcript isoform catalog of B. napus, which will facilitate genome reannotation, strengthen our understanding of the B. napus transcriptome and be applied for further functional genomic research.
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Affiliation(s)
- Shengli Yao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Fan Liang
- Nextomics Biosciences, Wuhan, 430000, Hubei, China
| | - Rafaqat Ali Gill
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Junyan Huang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan, 430062, Hubei, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan, 430062, Hubei, China
| | - Yueying Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan, 430062, Hubei, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan, 430062, Hubei, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan, 430062, Hubei, China
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Zhang H, Li G, Fu C, Duan S, Hu D, Guo X. Genome-wide identification, transcriptome analysis and alternative splicing events of Hsf family genes in maize. Sci Rep 2020; 10:8073. [PMID: 32415117 PMCID: PMC7229205 DOI: 10.1038/s41598-020-65068-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/26/2020] [Indexed: 12/13/2022] Open
Abstract
Heat shock transcription factor (Hsf) plays a transcriptional regulatory role in plants during heat stress and other abiotic stresses. 31 non-redundant ZmHsf genes from maize were identified and clustered in the reference genome sequenced by Single Molecule Real Time (SMRT). The amino acid length, chromosome location, and presence of functional domains and motifs of all ZmHsfs sequences were analyzed and determined. Phylogenetics and collinearity analyses reveal gene duplication events in Hsf family and collinearity blocks shared by maize, rice and sorghum. The results of RNA-Seq analysis of anthesis and post-anthesis periods in maize show different expression patterns of ZmHsf family members. Specially, ZmHsf26 of A2 subclass and ZmHsf23 of A6 subclass were distinctly up-regulated after heat shock (HS) at post-anthesis stage. Nanopore transcriptome sequencing of maize seedlings showed that alternative splicing (AS) events occur in ZmHsf04 and ZmHsf17 which belong to subclass A2 after heat shock. Through sequence alignment, semi-quantitative and quantitative RT-PCR, we found that intron retention events occur in response to heat shock, and newly splice isoforms, ZmHsf04-II and ZmHsf17-II, were transcribed. Both new isoforms contain several premature termination codons in their introns which may lead to early termination of translation. The ZmHsf04 expression was highly increased than that of ZmHsf17, and the up-regulation of ZmHsf04-I transcription level were significantly higher than that of ZmHsf04-II after HS.
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Affiliation(s)
- Huaning Zhang
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China
| | - Guoliang Li
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China
| | - Cai Fu
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China
| | - Shuonan Duan
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China
| | - Dong Hu
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China.
| | - Xiulin Guo
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, P.R. China.
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Wani SH, Kumar V, Khare T, Guddimalli R, Parveda M, Solymosi K, Suprasanna P, Kavi Kishor PB. Engineering salinity tolerance in plants: progress and prospects. PLANTA 2020; 251:76. [PMID: 32152761 DOI: 10.1007/s00425-020-03366-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/24/2020] [Indexed: 05/20/2023]
Abstract
There is a need to integrate conceptual framework based on the current understanding of salt stress responses with different approaches for manipulating and improving salt tolerance in crop plants. Soil salinity exerts significant constraints on global crop production, posing a serious challenge for plant breeders and biotechnologists. The classical transgenic approach for enhancing salinity tolerance in plants revolves by boosting endogenous defence mechanisms, often via a single-gene approach, and usually involves the enhanced synthesis of compatible osmolytes, antioxidants, polyamines, maintenance of hormone homeostasis, modification of transporters and/or regulatory proteins, including transcription factors and alternative splicing events. Occasionally, genetic manipulation of regulatory proteins or phytohormone levels confers salinity tolerance, but all these may cause undesired reduction in plant growth and/or yields. In this review, we present and evaluate novel and cutting-edge approaches for engineering salt tolerance in crop plants. First, we cover recent findings regarding the importance of regulatory proteins and transporters, and how they can be used to enhance salt tolerance in crop plants. We also evaluate the importance of halobiomes as a reservoir of genes that can be used for engineering salt tolerance in glycophytic crops. Additionally, the role of microRNAs as critical post-transcriptional regulators in plant adaptive responses to salt stress is reviewed and their use for engineering salt-tolerant crop plants is critically assessed. The potentials of alternative splicing mechanisms and targeted gene-editing technologies in understanding plant salt stress responses and developing salt-tolerant crop plants are also discussed.
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Affiliation(s)
- Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Anantnag, Jammu and Kashmir, 192 101, India.
| | - Vinay Kumar
- Department of Biotechnology, Modern College, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
- Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
| | - Tushar Khare
- Department of Biotechnology, Modern College, Savitribai Phule Pune University, Ganeshkhind, Pune, 411 016, India
| | | | | | - Katalin Solymosi
- Department of Plant Anatomy, Institute of Biology, ELTE-Eötvös Loránd University, Budapest, 1053, Hungary
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - P B Kavi Kishor
- Department of Biotechnology, Vignan's Foundation for Science Technology and Research, Vadlamudi, Guntur, 522 213, India
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Ding Y, Wang Y, Qiu C, Qian W, Xie H, Ding Z. Alternative splicing in tea plants was extensively triggered by drought, heat and their combined stresses. PeerJ 2020; 8:e8258. [PMID: 32030318 PMCID: PMC6995271 DOI: 10.7717/peerj.8258] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/20/2019] [Indexed: 11/20/2022] Open
Abstract
Drought and heat stresses can influence the expressions of genes, and thereby affect the growth and development of plants. Alternative splicing (AS) of genes plays crucial roles through increasing transcriptome diversity in plant stress responses. Tea plants, widely cultivated in the tropics and subtropics, are often simultaneously exposed to drought and heat stresses. In the present study, we performed a global transcriptome of tea leaves treated with drought, heat or their combination. In total, 19,019, 20,025 and 20,253 genes underwent AS in response to drought (DT), heat (HT) and their combined stress (HD), respectively, of which 12,178, 11,912 and 14,413 genes differentially spliced in response to DT, HT and HD, respectively. Also, 2,447 specific differentially spliced genes (DSGs) were found only in response to HD. All DSGs accounted for 48% of the annotated genes in tea tree genome. Comparison of DSGs and differentially expressive genes (DEGs) showed that the proportions of HT and HD-induced DSGs were 13.4% and 9.2%, while the proportion of DT increased to 28.1%. Moreover, the DEG-DSG overlapped genes tended to be enriched in a wide large of pathways in response to DT. The results indicated that the AS of genes in tea leaves was extensively triggered by drought, heat and their combined stresses. In addition, the AS enhanced the transcriptome adaption in response to drought and heat stresses, and the AS also provoked specific molecular functions in response to drought and heat synergy stress. The study might have practical significance for molecular genetic breeding of tea plants with stress resistance.
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Affiliation(s)
- Yiqian Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Chen Qiu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Wenjun Qian
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Hui Xie
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, China
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Li W, Wan XL, Yu JY, Wang KL, Zhang J. Genome-Wide Identification, Classification, and Expression Analysis of the Hsf Gene Family in Carnation ( Dianthus caryophyllus). Int J Mol Sci 2019; 20:ijms20205233. [PMID: 31652538 PMCID: PMC6829504 DOI: 10.3390/ijms20205233] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 01/26/2023] Open
Abstract
Heat shock transcription factors (Hsfs) are a class of important transcription factors (TFs) which play crucial roles in the protection of plants from damages caused by various abiotic stresses. The present study aimed to characterize the Hsf genes in carnation (Dianthus caryophyllus), which is one of the four largest cut flowers worldwide. In this study, a total of 17 non-redundant Hsf genes were identified from the D. caryophyllus genome. Specifically, the gene structure and motifs of each DcaHsf were comprehensively analyzed. Phylogenetic analysis of the DcaHsf family distinctly separated nine class A, seven class B, and one class C Hsf genes. Additionally, promoter analysis indicated that the DcaHsf promoters included various cis-acting elements that were related to stress, hormones, as well as development processes. In addition, cis-elements, such as STRE, MYB, and ABRE binding sites, were identified in the promoters of most DcaHsf genes. According to qRT-PCR data, the expression of DcaHsfs varied in eight tissues and six flowering stages and among different DcaHsfs, even in the same class. Moreover, DcaHsf-A1, A2a, A9a, B2a, B3a revealed their putative involvement in the early flowering stages. The time-course expression profile of DcaHsf during stress responses illustrated that all the DcaHsfs were heat- and drought-responsive, and almost all DcaHsfs were down-regulated by cold, salt, and abscisic acid (ABA) stress. Meanwhile, DcaHsf-A3, A7, A9a, A9b, B3a were primarily up-regulated at an early stage in response to salicylic acid (SA). This study provides an overview of the Hsf gene family in D. caryophyllus and a basis for the breeding of stress-resistant carnation.
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Affiliation(s)
- Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Xue-Li Wan
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Jia-Yu Yu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Kui-Ling Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Wang R, Liu H, Liu Z, Zou J, Meng J, Wang J. Genome-wide analysis of alternative splicing divergences between Brassica hexaploid and its parents. PLANTA 2019; 250:603-628. [PMID: 31139927 DOI: 10.1007/s00425-019-03198-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/24/2019] [Indexed: 05/23/2023]
Abstract
Compared with its parents, Brassica hexaploid underwent significant AS changes, which may provide diversified gene expression regulation patterns and could enhance its adaptability during evolution Polyploidization is considered a significant evolution force that promotes species formation. Alternative splicing (AS) plays a crucial role in multiple biological processes during plant growth and development. To explore the effects of allopolyploidization on the AS patterns of genes, a genome-wide AS analysis was performed by RNA-seq in Brassica hexaploid and its parents. In total, we found 7913 (27540 AS events), 14447 (70179 AS events), and 13205 (60804 AS events) AS genes in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. A total of 920 new AS genes were discovered in Brassica hexaploid. There were 56 differently spliced genes between Brassica hexaploid and its parents. In addition, most of the alternative 5' splice sites were located 4 bp upstream of the dominant 5' splice sites, and most of the alternative 3' splice sites were located 3 bp downstream of the dominant 3' splice sites in Brassica hexapliod, which was similar to B. carinata. Furthermore, we cloned and sequenced all amplicons from the RT-PCR products of GRP7/8, namely, Bol045859, Bol016025 and Bol02880. The three genes were found to produce AS transcripts in a new way. The AS patterns of genes were diverse between Brassica hexaploid and its parents, including the loss and gain of AS events. Allopolyploidization changed alternative splicing sites of pre-mRNAs in Brassica hexaploid, which brought about alterations in the sequences of transcripts. Our study provided novel insights into the AS patterns of genes in allopolyploid plants, which may provide a reference for the study of polyploidy adaptability.
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Affiliation(s)
- Ruihua Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Helian Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhengyi Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
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Li GL, Zhang HN, Shao H, Wang GY, Zhang YY, Zhang YJ, Zhao LN, Guo XL, Sheteiwy MS. ZmHsf05, a new heat shock transcription factor from Zea mays L. improves thermotolerance in Arabidopsis thaliana and rescues thermotolerance defects of the athsfa2 mutant. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:375-384. [PMID: 31128708 DOI: 10.1016/j.plantsci.2019.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 05/05/2023]
Abstract
High temperature directly affects the yield and quality of crops. Plant Hsfs play vital roles in plant response to heat shock. In the present study, ZmHsf05 was isolated from maize (Zea mays L.) using homologous cloning methods. The sequencing analysis demonstrated that CDS of ZmHsf05 was 1080 bp length and encoded a protein containing 359 amino acids. The putative amino acid sequence of ZmHsf05 contained typical Hsf domains, such as DBD, OD, NLS and AHA motif. Subcellular localization assays displayed that the ZmHsf05 is localized to the nucleus. ZmHsf05 was expressed in many maize tissues and its expression level was increased by heat stress treatment. ZmHsf05 rescued the reduced thermotolerance of the athsfa2 mutant in Arabidopsis seedlings. Arabidopsis seedlings of ZmHsf05-overexpressing increased both the basal and acquired thermotolerances. After heat stress, the ZmHsf05-overexpressing lines showed enhanced survival rate and chlorophyll content compared with WT seedlings. The expression of Hsps was up-regulated in the ZmHsf05-overexpressing Arabidopsis lines after heat stress treatment. These results suggested that ZmHsf05 plays an important role in both basal and acquired thermotolerance in plants.
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Affiliation(s)
- Guo-Liang Li
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, PR China
| | - Hua-Ning Zhang
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, PR China
| | - Hongbo Shao
- Salt-soil Agricultural Center, Key Laboratory of Agricultural Environment in the Lower Reaches of Yangtze River Plain, Institute of Agriculture Resources and Environment, Jiangsu Academy of Agriculture Science(JAAS), Nanjing, 210014, PR China; College of Environment and Safety Engineering, Qingdao University of Science & Technology, Qingdao 266000, China; Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224002, PR China.
| | - Gui-Yan Wang
- Faculty of Agronomy, Hebei Agricultural University, Baoding, 071001, PR China.
| | - Yuan-Yuan Zhang
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, PR China; College of Life Science, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Yu-Jie Zhang
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, PR China; College of Agriculture and Forestry Science and Technology, Hebei North University, Zhangjiakou, 075000, PR China
| | - Li-Na Zhao
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, PR China; Faculty of Agronomy, Hebei Agricultural University, Baoding, 071001, PR China
| | - Xiu-Lin Guo
- Plant Genetic Engineering Center of Hebei Province/Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, PR China.
| | - Mohamed Salah Sheteiwy
- Salt-soil Agricultural Center, Key Laboratory of Agricultural Environment in the Lower Reaches of Yangtze River Plain, Institute of Agriculture Resources and Environment, Jiangsu Academy of Agriculture Science(JAAS), Nanjing, 210014, PR China
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Kuang X, Sun S, Wei J, Li Y, Sun C. Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis. BMC PLANT BIOLOGY 2019; 19:210. [PMID: 31113367 PMCID: PMC6530051 DOI: 10.1186/s12870-019-1809-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 04/29/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Taxus cuspidata is well known worldwide for its ability to produce Taxol, one of the top-selling natural anticancer drugs. However, current Taxol production cannot match the increasing needs of the market, and novel strategies should be considered to increase the supply of Taxol. Since the biosynthetic mechanism of Taxol remains largely unknown, elucidating this pathway in detail will be very helpful in exploring alternative methods for Taxol production. RESULTS Here, we sequenced Taxus cuspidata transcriptomes with next-generation sequencing (NGS) and third-generation sequencing (TGS) platforms. After correction with Illumina reads and removal of redundant reads, more than 180,000 nonredundant transcripts were generated from the raw Iso-Seq data. Using Cogent software and an alignment-based method, we identified a total of 139 cytochrome P450s (CYP450s), 31 BAHD acyltransferases (ACTs) and 1940 transcription factors (TFs). Based on phylogenetic and coexpression analysis, we identified 9 CYP450s and 7 BAHD ACTs as potential lead candidates for Taxol biosynthesis and 6 TFs that are possibly involved in the regulation of this process. Using coexpression analysis of genes known to be involved in Taxol biosynthesis, we elucidated the stem biosynthetic pathway. In addition, we analyzed the expression patterns of 12 characterized genes in the Taxol pathway and speculated that the isoprene precursors for Taxol biosynthesis were mainly synthesized via the MEP pathway. In addition, we found and confirmed that the alternative splicing patterns of some genes varied in different tissues, which may be an important tissue-specific method of posttranscriptional regulation. CONCLUSIONS A strategy was developed to generate corrected full-length or nearly full-length transcripts without assembly to ensure sequence accuracy, thus greatly improving the reliability of coexpression and phylogenetic analysis and greatly facilitating gene cloning and characterization. This strategy was successfully utilized to elucidate the Taxol biosynthetic pathway, which will greatly contribute to the goals of improving the Taxol content in Taxus spp. using molecular breeding or plant management strategies and synthesizing Taxol in microorganisms using synthetic biological technology.
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Affiliation(s)
- Xuejun Kuang
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 China
| | - Sijie Sun
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 China
| | - Jianhe Wei
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 China
| | - Ying Li
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 China
| | - Chao Sun
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 China
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Alternative splicing of ZmCCA1 mediates drought response in tropical maize. PLoS One 2019; 14:e0211623. [PMID: 30699185 PMCID: PMC6353190 DOI: 10.1371/journal.pone.0211623] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 01/17/2019] [Indexed: 11/19/2022] Open
Abstract
The circadian clock regulates numerous biological processes in plants, especially development and stress responses. CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) is one of the core components of the day–night rhythm response and is reportedly associated with ambient temperature in Arabidopsis thaliana. However, it remains unknown if alternative splicing of ZmCCA1 is modulated by external stress in maize, such as drought stress and photoperiod. Here, we identified three ZmCCA1 splice variants in the tropical maize line CML288, which are predicted to encode three different protein isoforms, i.e., ZmCCA1.1, ZmCCA1.2, and ZmCCA1.3, which all retain the MYB domain. In maize, the expression levels of ZmCCA1 splice variants were influenced by photoperiod, tissue type, and drought stress. In transgenic A. thaliana, ZmCCA1.1 may be more effective than ZmCCA1.3 in increasing drought tolerance while ZmCCA1.2 may have only a small effect on tolerance to drought stress. Additionally, although CCA1 genes have been found in many plant species, alternative CCA1 splicing events are known to occur in species-specific ways. Our study provides new sight to explore the function of ZmCCA1 splice variants’ response to abiotic stress, and clarify the linkage between circadian clock and environmental stress in maize.
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50
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Wei Y, Liu G, Chang Y, He C, Shi H. Heat shock transcription factor 3 regulates plant immune response through modulation of salicylic acid accumulation and signalling in cassava. MOLECULAR PLANT PATHOLOGY 2018; 19:2209-2220. [PMID: 29660238 PMCID: PMC6638013 DOI: 10.1111/mpp.12691] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/27/2018] [Accepted: 04/09/2018] [Indexed: 05/05/2023]
Abstract
As the terminal components of signal transduction, heat stress transcription factors (Hsfs) mediate the activation of multiple genes responsive to various stresses. However, the information and functional analysis are very limited in non-model plants, especially in cassava (Manihot esculenta), one of the most important crops in tropical areas. In this study, 32 MeHsfs were identified from the cassava genome; the evolutionary tree, gene structures and motifs were also analysed. Gene expression analysis found that MeHsfs were commonly regulated by Xanthomonas axonopodis pv. manihotis (Xam). Amongst these MeHsfs, MeHsf3 was specifically located in the cell nucleus and showed transcriptionally activated activity on heat stress elements (HSEs). Through transient expression in Nicotiana benthamiana leaves and virus-induced gene silencing (VIGS) in cassava, we identified the essential role of MeHsf3 in plant disease resistance, by regulating the transcripts of Enhanced Disease Susceptibility 1 (EDS1) and pathogen-related gene 4 (PR4). Notably, as regulators of defence susceptibility, MeEDS1 and MePR4 were identified as direct targets of MeHsf3. Moreover, the disease sensitivity of MeHsf3- and MeEDS1-silenced plants could be restored by exogenous salicylic acid (SA) treatment. Taken together, this study highlights the involvement of MeHsf3 in defence resistance through the transcriptional activation of MeEDS1 and MePR4.
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Affiliation(s)
- Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesInstitute of Tropical Agriculture and Forestry, Hainan UniversityHaikou 570228China
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesInstitute of Tropical Agriculture and Forestry, Hainan UniversityHaikou 570228China
| | - Yanli Chang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesInstitute of Tropical Agriculture and Forestry, Hainan UniversityHaikou 570228China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesInstitute of Tropical Agriculture and Forestry, Hainan UniversityHaikou 570228China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesInstitute of Tropical Agriculture and Forestry, Hainan UniversityHaikou 570228China
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